Significance

Although antibodies can normally be obtained against a wide variety of antigens, there are still hard targets, including weakly immunogenic epitopes, which are not readily amenable to existing production techniques. In addition, such techniques can be relatively time-consuming and costly, especially if the screening for a specific epitope is required. In this work we describe a rational design method that enables one to obtain antibodies targeting any specific epitope within a disordered protein or disordered region. We show that this method can be used to target three disordered proteins and peptides associated with neurodegenerative and systemic misfolding diseases.

Abstract

Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions.

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